Curriculum Vitæ
Yusu Wang
Department of Computer Science and Engineering
The Ohio State Univ.,
395 Dreese Lab, 2015 Neil Ave.
Columbus, OH 43210, USA
Phone: (614)-2921309
Fax: (614)-2922911
E-mail: [email protected]
WWW: http://www.cse.ohio-state.edu/~yusu/
Research Interests
Discrete and computational geometry. Computational and applied topology. Topological data analysis. Applications of topological / geometric methods to practical domains such as computational biology, geometric
modeling, visualization and computer graphics.
Education
2000 – 2004 Ph.D., Computer Science, Duke University, USA
Research supervised by Prof. Pankaj K. Agarwal and Prof. Herbert Edelsbrunner
Thesis title: Shape Representation and Analysis in Structural Biology Applications
(Received Best Dissertation Award, CS Dept, Duke U., 2004.)
1998 – 2000 M.Sc., Computer Science, Duke University, USA
Research supervised by Prof. Pankaj K. Agarwal
Thesis title: Fast Occlusion Culling Algorithms for Walkthrough Applications
1993 – 1998 B.Sc. (Graduated with Distinction), Computer Science, Tsinghua University, China
Thesis supervised by Prof. Zesheng Tang
Thesis title: Reconstruction of 3D Anatomical Structures from 2D Medical Images
Employment
2011 – present Associate Professor: Computer Science and Engineering, OSU.
2005 – 2011
Assistant Professor: Computer Science and Engineering, OSU.
2004 – 2005
Postdoctoral Fellow: Computer Science Department, Stanford University.
Honors & Awards
• Lumley Research Award, College of Engineering, OSU (2011)
• A Best Paper Award, Eurovis (2010)
• Top Reviewer for journal Computational Geometry: Theory and Applications (2008)
• National Science Foundation (NSF) Career Award (2008)
• Department of Energy (DOE) Early Career Award (2006)
• Dept. Best Ph.D Dissertation, Duke University (2004)
• Department service award, Duke University (2002 - 2003).
Funding and Grants
• AF: Small: Geometric Data Processing and Analysis via Light-weight Structures, National Science Foundation, CCF-1319406, single PI. $481, 393.00. (06/2013 – 06/2016).
• AF:small: analyzing spaces and scalar fields via point clouds, National Science Foundation, CCF-1116258,
co-PI. $499, 761.00. (06/2011–06/2015).
• AF: EAGER: Collaborative Research: Integration of Computational Geometry and Statistical Learning for
Modern Data Analysis, National Science Foundation, CCF-1048983, PI. $196, 000.00. (09/2010–09/2012).
• Similarity-Based Indexing and Integration of Protein Sequence and Structure Databases, National Science
Foundation, DBI-0750891, co-PI. $498, 117.00. (07/2008–07/2012).
• CAREER: Geometric and Topological Methods in Shape Analysis, with Applications in Molecular Biology,
National Science Foundation, CCF-0747082, single PI. $420, 000.00. (02/2008–02/2013).
• ECPI: Feature extraction, characterization, and visualization for protein interaction via geometric and
topological methods, Department of Energy. DE-FG02-06ER25735. single PI. $295, 073.00. (09/2006–
09/2009)
Publications
Book Chapters
[1] V. Natarajan, P. Koehl, Y. Wang, and B. Hamann. Visual analysis of biomolecular surfaces. In L. Linsen,
H. Hagen, and B. Hamann (editors), Mathematical Methods for Visualization in Medicine and Life Sciences.
Springer Verlag, Mathematics and Visualization, 237–256, 2008.
Journal Papers
[1] W. Harvey, I. Park, O. R¨
ubel, V. Pascucci, P-T. Bremer, C. Li and Y. Wang. A collaborative visual
analytics suite for protein folding research. J. Mol. Graph. Modelling (JMG), 53: 59–71 (2014).
[2] T. K. Dey and Y. Wang. Reeb graphs: approximation and persistence. Discrete and Computational Geometry (DCG), 49 (1): 46–73, 2013.
[3] H. Doraiswamy, N. Shivashankar, V. Natarajan and Y. Wang. Topological saliency. Computers & Graphics.
37(7): 787-799 (2013).
[4] H. Sun, A. Sacan, H. Ferhatosmanoglu, and Y. Wang. Smolign: A Spatial Motifs-Based Protein Multiple
Structural Alignment Method. IEEE/ACM Trans. Comput. Biology Bioinform. 9(1): 249-261 (2012).
[5] C. Luo, I. Safa, and Y. Wang. Feature-aware streamline generation of planar vector fields via topological
methods. Computers & Graphics. 36(6): 754-766 (2012).
[6] T. K. Dey, P. Ranjan, and Y. Wang. Eigen deformation of 3D models. The Visual Computer. 28(6-8):
585-595 (2012).
[7] T. K. Dey, J. Sun and Y. Wang. Approximating Cycles in a Shortest Basis of the First Homology Group
from Point Data. Inverse Problems., 27(9): 124004–124023, 2011.
[8] P. K. Agarwal, S. Har-Peled, M. Sharir and Y. Wang. Hausdorff distance under translation for points and
balls. ACM Trans. Alg., 6(4), 71.1–71.26, (2010).
[9] O. Busaryev, T. K. Dey and Y. Wang. Tracking a Generator by Persistence. Discrete Math., Alg. and
Appl., 2(4): 539-552 (2010).
[10] Y. Wang. Relations between two common types of rectangular tiling. Internal. J. Comput. Geom. Appl.,
108(6): 379–385, 2009.
[11] H. Sun, H. Ferhatosmanoglu, and Y. Wang. An enhanced partial order curve comparison algorithm and
its application to analyzing protein folding trajectories. BMC BioInformatics, 9:344–354, 2008.
[12] Y. Wang. Approximating nearest neighbors among triangles in convex position. Inf. Proc. Letters., 108(6):
379–385, 2008.
[13] L. J. Guibas and Y. Wang. Towards unsupervised segmentation of semi-rigid low-resolution molecular
surfaces. Algorithmica, 48(4):433–438, 2007.
[14] A. Sacan, O. Ozturk, H. Ferhatosmanoglu, and Y. Wang. LFM-Pro: A tool for detecting significant local
structural sites in proteins. Bioinformatics, 23(6):709–716, 2007.
[15] P. K. Agarwal, N. Mustafa, and Y. Wang. Efficient algorithms for contact-map overlap problem. J.
Comput. Biology (JCB), 14(2):131–143, 2007.
[16] H. Wu, M. Wong, I. Liu, and Y. Wang. Placement-proximity-based voltage island grouping under performance requirement. IEEE Trans. Computer-Aided Design, 26(7):1256–1269, 2007.
[17] V. Natarajan, Y. Wang, T. Bremer, V. Pascucci, and B. Hamann. Segmenting molecular surfaces. Computer Aided Geometric Design (CAGD), pages 495–509, 2006.
[18] P. K. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang. Extreme elevation on a 2-manifold. Discrete and
Computational Geometry (DCG), 36(4):553–572, 2006.
[19] P. K. Agarwal, Y. Wang, and H. Yu. A 2D kinetic triangulation with near-quadratic topological changes.
Discrete and Computational Geometry (DCG), 36(4):573–592, 2006.
[20] P. K. Agarwal, S. Har-Peled, N. Mustafa, and Y. Wang. Near-linear time approximation algorithms for
curve simplification. Algorithmica, 42(3/4):203–221, 2005.
[21] P. K. Agarwal, H. Edelsbrunner, and Y. Wang. Computing the writhing number of a polygonal knot.
Discrete and Computational Geometry, 32(1):37–53, 2004.
[22] S. Har-Peled and Y. Wang. Shape fitting with outliers. SIAM Journal on Computing, 33(2):269–285, 2004.
Refereed Conferences
Note: publications in certain graphics venues, (specifically, SIGGRAPH, SIGGRAPH Asia, and Sympos.
Geom. Processing,) also appeared in special issues of some journals (specifically, in ACM Trans. Graph.
and Comput. Graph. Forum). These publications are only listed once below, and not listed in the section for
Journal publications.
[1] Q. Que, M. Belkin and Y. Wang. Learning with Fredholm kernels. In Neural Information Processing
Systems (NIPS), To appear, 2014.
[2] U. Bauer, X. Ge and Y. Wang. Measuring distance between Reeb graphs. In Proc. 29th Annu. ACM
Sympos. Comput. Geom. (SoCG), pages 464–473, 2014.
[3] S. Wang, Y. Wang and R. Wenger. The JS-Graph of merge and split trees. In Proc. 29th Annu. ACM
Sympos. Comput. Geom. (SoCG), pages 539–548, 2014.
[4] T. K. Dey, F. Fan and Y. Wang. Computing Topological Persistence for Simplicial Maps. In Proc. 29th
Annu. ACM Sympos. Comput. Geom. (SoCG), pages 345–354, 2014.
[5] J. Chen, X. Ge, L. Wei, B. Wang, Y. Wang, H. Wang, Y. Fei, K. Qian, J. Yong, W. Wang. Bilateral blue
noise sampling. In SIGGRAPH Asia), also appeared in a special issue of the journal ACM Trans. Graph.,
32(6): 216, 2013.
[6] T. K. Dey, F. Fan and Y. Wang. An efficient computation of handle and tunnel loops via Reeb graphs. In
SIGGRAPH 2013), also appeared in a special issue of the journal ACM Trans. Graph., 32(4): 32, 2013.
[7] E. W. Chambers and Y. Wang. Measuring similarity between curves on 2-manifolds via homotopy area.
In Proc. 28th Annu. ACM Sympos. Comput. Geom. (SoCG), pages 425–434, 2013.
[8] T. K. Dey, F. Fan and Y. Wang. Graph induced complex on point data. In Proc. 28th Annu. ACM Sympos.
Comput. Geom. (SoCG), pages 107–116, 2013.
[9] T. K. Dey, P. Ranjan and Y. Wang. Weighted Graph Laplace Operator under Topological Noise. In Proc.
24th ACM-SIAM Sympos. Discrete Alg. (SoDA), pages 197–208, 2013.
[10] M. Belkin, Q. Que, Y. Wang and X. Zhou. Towards understading complex spaces: graph Laplacians on
manifolds with singularities and boundaries. In 25th Conf. Learning Theory (COLT), Journal of Machine
Learning Research – Proceedings Track 23, pages 36.1–36.26, 2012.
[11] T. K. Dey, X. Ge, Q. Que, I. Safa, L. Wang, and Y. Wang. Feature-Preserving Reconstruction of Singular
Surfaces. In Sympos. Geom. Processing., also appeared in a special issue of the journal Comput. Graph.
Forum, 31(5): 1787-1796, 2012.
[12] O. Busaryev, S. Cabello, C. Chen, T. K. Dey and Y. Wang. Annotating Simplices with a Homology Basis
and Its Applications. In SWAT, pages 189–200, 2012.
[13] X. Ge, I. Safa, M. Belkin, and Y. Wang. Data Skelentonization via Reeb Graphs. In Proc. 25th Annu.
Conf. Neural Information Processing Systems (NIPS), pages 837–845, 2011.
[14] T. K. Dey and Y. Wang. Reeb graphs: approximation and persistence. In Proc. 26th Annu. ACM Sympos.
Comput. Geom. (SoCG), pages 226–235, 2011.
[15] W. Harvey and Y. Wang Generating and exploring a collection of topological landscapes for visualization
of scalar-valued functions. Eurographics/IEEE Sympos. Visualization, also appeared in a special issue of
the journal Comput. Graph. Forum, 29 (3): 993–1002, 2010. Received a Best Paper Award.
[16] W. Harvey and Y. Wang. A Randomized O(m log m) Time Algorithm for Computing Reeb Graph of
Arbitrary Simplicial Complexes. Proc. 25th Annu. ACM Sympos. Compu. Geom. (SoCG), pages 267–276,
2010.
[17] T. K. Dey and J. Sun and Y. Wang. Approximating Loops in a Shortest Homology Basis from Point Data
Proc. 25th Annu. ACM Sympos. Compu. Geom. (SoCG), pages 166–175, 2010.
[18] T. K. Dey, P. Rajan, and Y. Wang. Convergence, Stability, and Discrete Approximation of Laplace
Spectra. In Proc. 21st ACM-SIAM Sympos. Discrete Alg. (SoDA), pages 650–663, 2010.
[19] T. K. Dey and K. Li and C. Luo and P. Rajan and I. Safa and Y. Wang. Persistent heat signature for
pose-oblivious matching of incomplete models. In Sympos. Geom. Processing, also appeared in a special
issue of the journal Comput. Graph. Forum, 29 (5): 1545–1554, 2010 .
[20] O. Busaryev, T. K. Dey and Y. Wang. Tracking a Generator by Persistence. In COCOON, pages 278–287,
2010.
[21] C. Luo, I. Safa, and Y. Wang. Estimating Gradients from Meshes and Point Clouds via Diffusion Metrics.
In Sympos. Geom. Process., also appeared in a special issue of the journal Comput. Graph. Forum, 28 (5):
1497–1508, 2009.
[22] C. Luo, J. Sun, and Y. Wang. Integral estimation from point clouds in d-dimensional space: A geometric
view. In Proc. 24th Annu. ACM Sympos. Comput. Geom., pages 116–124, 2009.
[23] M. Belkin, J. Sun, and Y. Wang. Constructing Laplace operator from point clouds in Rd . In Proc. 20th
ACM-SIAM Sympos. Discrete Algorithms, pages 1031–1040, 2009.
[24] K. Buchin, M. Buchin, and Y. Wang. Exact partial curve matching under the Frechet distance. In Proc.
20th ACM-SIAM Sympos. Discrete Algorithms, pages 645–654, 2009.
[25] M. Belkin, J. Sun, and Y. Wang. Discrete Laplace Operator for Meshed Surfaces. In Proc. 24th Annu.
ACM Sympos. Comput. Geom., pages 278–287, 2008.
[26] Z. Zheng, K. Fan, P. Sinha, and Y. Wang. Distributed roadmap aided routing in sensor networks. In
IEEE MASS, pages 347–352, 2008.
[27] H. Sun, H. Ferhatosmanoglu, M. Ota, and Y. Wang. Enhanced partial order curve comparison over
multiple protein folding trajectories. In Proc. Intl. Conf. Computational System Bioinformatics, pages
299–310, 2007.
[28] Y. Wang. Relations between two common types of rectangular tiling. In Intl. Symp. Algorithms and
Computation, pages 193–202, 2006.
[29] B. Aronov, S. Har-Peled, C. Kauner, C. Wenk, and Y. Wang. Fr´echet distance for curves revisited. In
Proc. 14th Annu. European Sympos. Algorithms, pages 52–63, 2006.
[30] S. Funke, L. Guibas, A. Nguyen, and Y. Wang. Distance-sensitive routing and information brokerage in
sensor networks. In Intl. Conf. Distributed Computing in Sensor Systems, pages 234–251, 2006.
[31] Y. Wang and L. J. Guibas. Towards unsupervised segmentation of semi-rigid low-resolution molecular
surfaces. In Geometric Modeling and Processing, pages 129–142, 2006.
[32] H. Wu, I. Liu, M. Wong, and Y. Wang. Post-placement voltage island generation under performance
requirement. In Intl. Conf. Computer Aided Design, pages 309–316, 2005.
[33] Y. Wang, P. K. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph. Coarse and reliable geometric
alignment for protein docking. In Pacific Symposium on Biocomputing, pages 66–77, 2005.
[34] P. K. Agarwal, Y. Wang, and P. Yin. Lower bound for sparse euclidean spanners. In Proc. 16th ACM-SIAM
Sympos. Discrete Algorithms, pages 670–671, 2005.
[35] P. K. Agarwal, Y. Wang, and H. Yu. A 2D kinetic triangulation with near-quadratic topological changes.
In Proc. 20th Annu. ACM Sympos. Comput. Geom., pages 180–189, 2004.
[36] P. K. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang. Extreme elevation on a 2-manifold. In Proc.
20th Annu. ACM Sympos. Comput. Geom., pages 357–365, 2004.
[37] P. K. Agarwal, S. Har-Peled, M. Sharir, and Y. Wang. Hausdorff distance under translation for points
and balls. In Proc. 19th Annu. ACM Sympos. Comput. Geom., pages 282–291, 2003.
[38] S. Har-Peled and Y. Wang. Shape fitting with outliers. In Proc. 19th Annu. ACM Sympos. Comput.
Geom., pages 29–38, 2003.
[39] P. K. Agarwal, H. Edelsbrunner, and Y. Wang. Computing the writhing number of a polygonal knot. In
Proc. 13th ACM-SIAM Sympos. Discrete Algorithms, pages 791–799, 2002.
[40] P. K. Agarwal, S. Har-Peled, N. Mustafa, and Y. Wang. Near-linear time approximation algorithms for
curve simplification. In Proc. 10th Annu. European Sympos. Algorithms, pages 29 – 41, 2002.
[41] Y. Wang, P. K. Agarwal, and S. Har-Peled. An on-line occlusion culling algorithm for fast walkthrough
in urban areas. In Eurographics, 2001.
Software Packages Developed
Denali: A software package for visulizing and exploring high-dimensional data using a terrain metaphor.
Developed by PhD student J. Eldridge. Software, tutorial, documentation can be downloaded at
http://denali.cse.ohio-state.edu/ .
Ayla: A visual analytic platform for exploring high-dimensional molecular simulation data.
Developed by PhD student W. Harvey.
Software and documentation can be downloaded at
http://aylasoftware.nfshost.com/.
Smolign, EPO, LFM-Pro: Software packages for comparing multiple protein structures, and for detecting
local structural sites in proteins. Software can be downloaded at http://bio.cse.ohio-state.edu/.
Other: I maintain code such as for computing Reeb graph, discrete Laplace operator, and for metric graph
reconstruction, on my webpage, next to the reference of respective papers.
Professional Service
Editorial board:
Journal of Computatoinal Geometry.
Program committee:
SIAM / ACM Symposium on Discrete Algorithms (SoDA), 2015.
ACM Symposium on Computational Geometry, Video Track, 2014.
Intl. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2014.
Symposium on Experimental Algorithms 2014.
CG Week workshops associated with SoCG 2013.
ACM Symposium on Computational Geometry (SoCG) 2012.
European Symposium on Algorithms 2010.
SIAM workshop on Algorithm Engineering and Experiments 2010.
ACM Symposium on Computational Geometry 2006.
Organization activities:
Co-organizor of AMS (American Math Society)-sponsored MRC summer conference on Discrete and
Computational Geometry, June 10–16, Snowbird, Utah. 2012
Refereeing:
Journals: Algorithmica, CAGD, CGF, CGTA, DCG, FoCM, IJCGA, SICOMP, TCBB, TVCG, IEEE
Trans. Comput. Bio and Bioinformatics, etc.
Conferences: FOCS, SOCG, STOC, SODA, SIGGRAPH, IEEE Visualiation, EuroVis, RECOMB, ISMB,
SGP, ESA, etc.
Grant review:
NSF panel reviews; U.S.-Israel Binational Science Foundation grant reviews.
Other activities:
Short course lecturer on ”Some topics in computational topology” at AMS Annual Joint Mathematics
Meeting, Baltimore, 2014.
Student Supervision and Mentoring
PostDocs mentored:
Ahmet Sacan (co-supervised with Dr. Hakan Ferhatosmanoglu): Currently an Assistant Professor at
Drexel University.
PhD students supervised:
Hong Sun (co-advised with Dr. H. Ferhatosmanoglu): First position: research scientist in SRA, InC,
NIEHS, North Carolina.
Issam Safa: First position: Intel, Portland.
William Harvey: First position: Postdoc at Research Institute at Nationwide Childrens Hospital.
Chuanjiang Luo: First position: Google Inc, New York.
Pawas Ranjan (co-advised with Dr. T. K. Dey): First position: Microsoft, India.
Fengtao Fan (co-advised with Dr. T. K. Dey): First position: Google Inc., San Jose.
Suyi Wang and Xiaoyin Ge : current PhD student.
Dayu Shi and Zhe Dong: current PhD students co-advised with Dr. T. K. Dey.
Selected Recent Invited Presentations (since 2012)
1. Reeb graphs, Approximation and Stability, 48th Spring Topology and Dynamics Conference, Richmond,
VA, 2014. Plenary speaker.
2. Spectral Point Clouds Procesing Based on Laplace-Beltrami Operator, Workshop SIGMA at CIRM, Marseille, France, 2012. Plenary speaker.
3. Data Sparsification for Homology Inference, Workshop on Topological Data Analysis, Kyoto University,
Japan, 2014.
4. Data Sparsification for Homology Inference, SAMSI (Statistical and Applied Mathematical Scienes Institute) Workshop on LDHD: Topological data analysis. 2014.
5. Visualizing and Exploring Molecular Simulation Data via Protein Energy Landscape Metaphor, IMA
Workshop on Topological structures in computational biology. 2013.
6. Measuring Distance Between Reeb Graphs, IMA Workshop on Modern applications of homology and
cohomology. 2013.
7. Understanding the Gaussian-weighted Graph Laplacian, Dagstuhl Workshop on Computational Geometry,
Dagstuhl School, Germany, 2013.
8. Visualizing and Exploring Molecular Simulation Data via Protein Energy Landscape Metaphor, Joint
BioMaPS and Applied Topology Seminar, Rutgers University, 2013.
9. Using Gaussian-Weighted Graph Laplacian for Geometric Shape Processing, Minisymposiusm on Applications to Image Processing and Shape Analysis, SIAM Conference on Applied Algebraic Geometry.
2013.
10. Understanding the Gaussian-weighted Graph Laplacian, Geometry/Topology Seminar at Institute of Science and Technology (IST), Austria, 2012.
11. Laplace Operator from Discrete Samples and Applications, Seminar, INRIA Saclay, 2012.
12. Understanding the Gaussian-weighted Graph Laplacian, BIRS (Banff International Research Station)
Workshop on Topological data analysis and machine learning theory. 2012.
13. Towards understanding more complex data – singular manifolds reconstruction, 3-D Geometry / Imaging
Conference, Kunming, China. 2012.
14. Towards understanding more complexity data – Graph Laplacians on singular manifolds, SIAM minisymposium on computational geometry in AMS/Joint Mathematics Meetings, Boston, 2012.
15. Reeb Graphs: Approximation an Persistence, AMS regional meeting, Akron, Ohio. 2012.